Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 3 of 316
Found at i:625567 original size:137 final size:137
Alignment explanation
Indices: 625403--625675 Score: 447
Period size: 137 Copynumber: 2.0 Consensus size: 137
625393 CTTCCTACAT
*
625403 TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGA
1 TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGA
* **
625468 CAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTTTCG
66 CAAAAGATCTTGCCTTCCTACATTGACAACGAAGCAGATCGAAAACACAAACCTTGCCTCCCTCG
625533 GTTGTGA
131 GTTGTGA
* * *
625540 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
1 TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGA
* * * *
625605 CAAAAGATCTTGTCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCG
66 CAAAAGATCTTGCCTTCCTACATTGACAACGAAGCAGATCGAAAACACAAACCTTGCCTCCCTCG
625670 GTTGTG
131 GTTGTG
625676 GTGGAGCTAG
Statistics
Matches: 125, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 125 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (137 bp):
TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGA
CAAAAGATCTTGCCTTCCTACATTGACAACGAAGCAGATCGAAAACACAAACCTTGCCTCCCTCG
GTTGTGA
Found at i:625642 original size:88 final size:87
Alignment explanation
Indices: 625540--625953 Score: 437
Period size: 88 Copynumber: 4.7 Consensus size: 87
625530 TCGGTTGTGA
625540 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
1 TGACAGCGAAGCAGGTCGAAGA-ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
* *
625605 CAAAAGATCTTGTCTTCCTGCAT
65 CAACAGATCTTGCCTTCCTGCAT
* * * *
625628 TGACAACGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTGTGGTGGAGCTAGTTGAAGA
1 TGACAGCGAAGCAGGTCGAAGA-ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
* *
625693 TAGCAGATCTTGCCTTCCTGCAT
65 CAACAGATCTTGCCTTCCTGCAT
* * * * * *
625716 TAACAGCGAAGTAGATCGAAAAACAAAGCCTTGCCTC-CATCGGTTG-CAGTAGAGCTGGTTGAA
1 TGACAGCGAAGCAGGTCGAAGAACAAA-CCTTGCCTCTC-TCGGTTGTGA-TGGAGCTGGTTGAA
* * * *
625779 GATAGCAGATCTTGCCTTCCTACGT
63 GACAACAGATCTTGCCTTCCTGCAT
* * * *
625804 TAACAGCGAAGCAGATCGAA-AACAAAGCCTTGCCTCTCTCGAG-TGTAGA-AGAGTTGGTTGAA
1 TGACAGCGAAGCAGGTCGAAGAACAAA-CCTTGCCTCTCTCG-GTTGT-GATGGAGCTGGTTGAA
* * ** *
625866 GACAACTGATTTTATCTTCCTGCGT
63 GACAACAGATCTTGCCTTCCTGCAT
* *
625891 TGACAGTGAAGCAGGTCGAAG-ACAAACCTTACCTCTCTCGGTTGT-AGTGGAGCTGGTTGAAGA
1 TGACAGCGAAGCAGGTCGAAGAACAAACCTTGCCTCTCTCGGTTGTGA-TGGAGCTGGTTGAAGA
625954 ATTACAGATC
Statistics
Matches: 280, Mismatches: 35, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
84 1 0.00
85 1 0.00
86 29 0.10
87 79 0.28
88 169 0.60
89 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (87 bp):
TGACAGCGAAGCAGGTCGAAGAACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGAC
AACAGATCTTGCCTTCCTGCAT
Found at i:625706 original size:225 final size:225
Alignment explanation
Indices: 625315--625761 Score: 680
Period size: 225 Copynumber: 2.0 Consensus size: 225
625305 CTTCCTACAT
*
625315 TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGA
1 TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGA
* **
625380 CAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTTTCG
66 CAAAAGATCTTGCCTTCCTACATTGACAACGAAGCAGATCGAAAACACAAACCTTGCCTCCCTCG
* *
625445 GTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGA
131 GTTGTGATAGAGCTAGTTGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGA
**
625510 AAACACAAA-CCTTGCCTCTTTCGGTTGTGA
196 AAA-ACAAAGCCTTGCCTCCATCGGTTGTGA
* * *
625540 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGA
1 TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGA
* * * *
625605 CAAAAGATCTTGTCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCG
66 CAAAAGATCTTGCCTTCCTACATTGACAACGAAGCAGATCGAAAACACAAACCTTGCCTCCCTCG
* * * ** * *
625670 GTTGTGGTGGAGCTAGTTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGA
131 GTTGTGATAGAGCTAGTTGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGA
625735 AAAACAAAGCCTTGCCTCCATCGGTTG
196 AAAACAAAGCCTTGCCTCCATCGGTTG
625762 CAGTAGAGCT
Statistics
Matches: 199, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
224 5 0.03
225 194 0.97
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (225 bp):
TGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGA
CAAAAGATCTTGCCTTCCTACATTGACAACGAAGCAGATCGAAAACACAAACCTTGCCTCCCTCG
GTTGTGATAGAGCTAGTTGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGA
AAAACAAAGCCTTGCCTCCATCGGTTGTGA
Found at i:627706 original size:3 final size:3
Alignment explanation
Indices: 627695--627735 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
627685 ATTATTTTGT
627695 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT
627736 TGTTTATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:628269 original size:16 final size:16
Alignment explanation
Indices: 628250--628280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
628240 TACACCCATA
*
628250 TATATGTACATATTTT
1 TATATATACATATTTT
628266 TATATATACATATTT
1 TATATATACATATTT
628281 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:651059 original size:16 final size:16
Alignment explanation
Indices: 651038--651071 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
651028 ATCAAAGTCA
*
651038 AATATATTATGCTAAT
1 AATATATCATGCTAAT
*
651054 AATATATCATTCTAAT
1 AATATATCATGCTAAT
651070 AA
1 AA
651072 ATGCTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATATCATGCTAAT
Found at i:651084 original size:24 final size:24
Alignment explanation
Indices: 651054--651104 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
651044 TTATGCTAAT
* *
651054 AATATATCATTCTAATAAATGCTA
1 AATATATCATACTAATAAATACTA
* *
651078 AATATATTATACTTATAAATACTA
1 AATATATCATACTAATAAATACTA
651102 AAT
1 AAT
651105 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATATCATACTAATAAATACTA
Found at i:653049 original size:17 final size:17
Alignment explanation
Indices: 653027--653059 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
653017 TTTTAAAAAT
653027 TATAAA-ATATAAATTAA
1 TATAAAGATA-AAATTAA
653044 TATAAAGATAAAATTA
1 TATAAAGATAAAATTA
653060 CATTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TATAAAGATAAAATTAA
Found at i:653942 original size:143 final size:136
Alignment explanation
Indices: 653771--655394 Score: 786
Period size: 145 Copynumber: 11.8 Consensus size: 136
653761 ATGACAAAAT
653771 TATATATTTTGTTGTTTGGTTA-GTTAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTAT
1 TATATATTTTGTTGTTTGGTTACG-TAGAAAGTAAATT-AAGTGGATTAAGCTTAATTTAGCTAT
* * * *
653835 TTTAATTGTCTAAATTTGGTCATTTAGCTG-AAAATTTTAGTGTTCTTTTGTTATTAATAAGTTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTC---T-TT-TTAAT--GGTT
*
653899 CTTTATGAATATATG
122 CTTTATGAATATAAG
* * * *
653914 TATATATTTTATTGTTTGGTTACGTAGAAAGTAAATTAAAGTGGATTAAGTTTAATTTAACCATT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATT-AAGTGGATTAAGCTTAATTTAGCTATT
* * **
653979 TTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGA
65 TTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
654044 ATATAAG
130 ATATAAG
* * * *
654051 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTATT
* * ***** *
654116 TTAGTTGTCGTGAAA-----AAATTTAG-TG-TTCTTTTTGGTGGTTC---TT--T--------A
65 TTAATTGTC-T-AAATTTCGTAATTTAGCTGAAAAAATTTAGT-GTTCTTTTTAATGGTTCTTTA
654161 TGAATATAAG
127 TGAATATAAG
* * * * *
654171 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGATACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTATT
* * * ** ** *
654236 TTAGTTGTCGGGAAA-----AAATTTAG-TG-TTATTTTTGGTGGTTC---TT--T--------A
65 TTAATTGTC--TAAATTTCGTAATTTAGCTGAAAAAATTTAGT-GTTCTTTTTAATGGTTCTTTA
654281 TGAATATAAG
127 TGAATATAAG
* * * *
654291 TATATTTTTTGTTGTTTGGTTACTTAGAAAGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAA-TTAAGTGGATTAAGCTTAATTTAGCTATT
* * * * * * **
654356 TTAATCGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATTTTGGTGGTTCTTTATGA
65 TTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
654421 ATATAAG
130 ATATAAG
* * * * *
654428 TATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTATAGTGGAATAAGCTT-ATGTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAAT-TTAGCTAT
* * * * *
654492 TTTAATT-TCTAAGTTTGGTCATTTAGGTGAAAAACA-TTAGTGTTCTTCTGCTTTTTTTTTATG
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAA-ATTTAGTG----T-T-C---TTTTTAATG
*
654555 GTTCTTTATGAATATATG
119 GTTCTTTATGAATATAAG
* * * *
654573 TATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGA-TAAGCTTAATTTACACTA
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGT-GGATTAAGCTTAATTTA-GCTA
* * * * ** *
654637 CTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA--T--TGTTATTAGTAA-GTTTCTTTAT
63 TTTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTAT
**
654697 GAAT-TGATC
128 GAATAT-AAG
* ** **
654706 TATATGTTTTGTTGTTTGGTTATTTAGAAAGTAAATGGT-AGTGGGA-TAAGCTTAA-GAATGCT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAAT--TAAGT-GGATTAAGCTTAATTTA-GCT
* * * * * * * * *
654768 ACTTTAGTTTTCTAAATTTCGTTACTTAGGTGACAAAAGTTAGTGTTCTTATGCTATTTTTTATG
62 ATTTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTG----T-T-C--TTTTTAATG
* *
654833 GTTCATTATGAATATATG
119 GTTCTTTATGAATATAAG
* * * * * *
654851 TATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGA-TAACCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGT-GGATTAAGCTTAATTTAGCTAT
* * * * * * * *
654915 TTTACTTTTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTGTCTTTTGTTTTTTTTTTATAGT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTA--G-----TG-TTCTTTTTAATGGT
*
654980 TCTTTATGAATAT--C
121 TCTTTATGAATATAAG
* * * *
654994 TTTATA-TTTGTTGTTTGGTTACTTAGAAAGTAAATTATAATGGATTGAGCTTAATTTAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTA-T
* * ** * *
655058 TTT-ATTGTCTAAATTTCGTCATTTAGGTGAAAACTTTTTGTGTTCTTTTGTTATTAGCAAGTTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTC-TTT-TTAAT-G---G-TT
**
655122 CTTTATGAATATGTG
122 CTTTATGAATATAAG
* * * * * *
655137 TATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGGA-TAAGCTTAATTTAACTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATT-AAGT-GGATTAAGCTTAATTTAGCTAT
** * * * * * **
655201 TTTAATTGTCTAAATTTCGTCGTTTAGGTAAAAAAATTTCGTGTTTCTTTTGTTATTAGTAAGTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTG-TTC-TTT-TTAATGGT-TCTT
* *
655266 TATGCACAAACATATG
125 TATG----AATATAAG
* * * * * *
655282 TATATA--TTGCCT-TTTGGTTGCTTAGAAAGTAAATTATGGTGGAATAAGCTTAATTTAGCTAC
1 TATATATTTTG-TTGTTTGGTTACGTAGAAAGTAAATTA-AGTGGATTAAGCTTAATTTAGCTAT
* * * *
655344 TTTAATTGTCCAAATTTCGTTATTTAGGTG-AAAAATTTAAATGTTCTTTTT
64 TTTAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTT-AGTGTTCTTTTT
655395 GTTTTTTTGG
Statistics
Matches: 1222, Mismatches: 163, Indels: 195
0.77 0.10 0.12
Matches are distributed among these distances:
118 2 0.00
120 190 0.16
121 3 0.00
123 6 0.00
124 6 0.00
125 7 0.01
127 2 0.00
128 1 0.00
129 1 0.00
130 2 0.00
132 42 0.03
133 69 0.06
134 14 0.01
135 6 0.00
136 40 0.03
137 150 0.12
138 2 0.00
139 6 0.00
140 9 0.01
141 30 0.02
142 90 0.07
143 173 0.14
144 99 0.08
145 222 0.18
146 19 0.02
147 26 0.02
148 1 0.00
149 2 0.00
152 2 0.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (136 bp):
TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTAAGTGGATTAAGCTTAATTTAGCTATTT
TAATTGTCTAAATTTCGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGAA
TATAAG
Found at i:654095 original size:137 final size:137
Alignment explanation
Indices: 653771--654124 Score: 433
Period size: 143 Copynumber: 2.5 Consensus size: 137
653761 ATGACAAAAT
* *
653771 TATATATTTTGTTGTTTGGTTAGTTAGAAAGTAAATTGA-AGTGGATTAAGCTTAATTTAGCTAT
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATTTAGCTAC
* * * *
653835 TTTAATTGTCTAAATTTGGTCATTTAGCTG-AAAATTTTAGTGTTCTTTTGTTATTAATAAGTTT
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTC---T-TT-TTAAT--GGTT
653899 CTTTATGAATATATG
123 CTTTATGAATATATG
* * * * * * *
653914 TATATATTTTATTGTTTGGTTACGTAGAAAGTAAATTAAAGTGGATTAAGTTTAATTTAACCATT
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACT
* * **
653979 TTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGA
66 TTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
*
654044 ATATAAG
131 ATATATG
* *
654051 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACT
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACT
*
654116 TTAGTTGTC
66 TTAATTGTC
654125 GTGAAAAAAT
Statistics
Matches: 184, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
137 81 0.44
139 3 0.02
140 2 0.01
141 1 0.01
142 1 0.01
143 82 0.45
144 14 0.08
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (137 bp):
TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACT
TTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
ATATATG
Found at i:654218 original size:120 final size:120
Alignment explanation
Indices: 654005--654358 Score: 645
Period size: 120 Copynumber: 3.0 Consensus size: 120
653995 CGTAATTTAG
654005 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
1 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
654070 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
654125 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
1 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
*
654190 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGATACTTTAGTTGTC
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
* * * *
654245 GGGAAAAAATTTAGTGTTATTTTTGGTGGTTCTTTATGAATATAAGTATATTTTTTGTTGTTTGG
1 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
* *
654310 TTACTTAGAAAGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACTTTA
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTA
654359 ATCGTCTCAA
Statistics
Matches: 226, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 226 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (120 bp):
GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
Found at i:654601 original size:145 final size:143
Alignment explanation
Indices: 654408--655402 Score: 956
Period size: 145 Copynumber: 7.0 Consensus size: 143
654398 TTCATTTTGG
* * *
654408 TGGTTCTTTATGAATATAAGTATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATTATAGTGGA
1 TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
* *
654473 ATAAGCTT-ATGTTAGCTACTTTAATT-TCTAAGTTTGGTCATTTAGGTGAAAAACATTAGTGTT
66 ATAAGCTTAAT-TTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA-ATTAGTGTT
*
654536 CTTCTGCTTTTTTTTTA
129 CTTTTG--TTTTTTTTA
*
654553 TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGG
1 TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
*
654618 ATAAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA-T--TGTT-
66 ATAAGCTTAATTTA-GCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTAGTGTTC
* *
654679 ATTAG-------TA
130 TTTTGTTTTTTTTA
* * * ** * **
654686 AGTTTCTTTATGAAT-TGATCTATATGTTTTGTTGTTTGGTTATTTAGAAAGTAAATGGTAGTGG
1 TGGTTCTTTATGAATAT-ATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGG
** * * * * *
654750 GATAAGCTTAA-GAATGCTACTTTAGTTTTCTAAATTTCGTTACTTAGGTGACAAAAGTTAGTGT
65 GATAAGCTTAATTTA-GCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGA-AAAAATTAGTGT
* *
654814 TCTTATGCTATTTTTTA
128 TCTTTTG-TTTTTTTTA
* * * * *
654831 TGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGG
1 TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
* * * *
654896 ATAACCTTAATTTAGCTACTTTACTTTTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTG-TC
66 ATAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA-TTAGTGTTC
654960 TTTTGTTTTTTTTTTA
130 TTTTG--TTTTTTTTA
* * *
654976 TAGTTCTTTATGAATATCT-T-TAT-ATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAAT-GG
1 TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
* * ** *
655037 ATTGAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTCATTTAGGTGAAAACTTTTTGTGTT
66 A-TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAA-AATTAGTGTT
* ***
655102 CTTTTGTTATTAGCA
129 CTTTTGTTTTTTTTA
* * * * * * *
655117 AGTTTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGG
1 TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
* * * *
655182 ATAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCGTTTAGGTAAAAAAATTTCGTGTTT
66 ATAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA-TTAGTG-TT
* **
655247 CTTTTGTTATTAGTA
129 CTTTTGTTTTTTTTA
* * * ** ** * * * *
655262 AGTTTATGCACAAACATATGTATAT-A-TTGCCT-TTTGGTTGCTTAGAAAGTAAATTATGGTGG
1 TGGTTCTTTATGAATATATGTATATAATTTG-TTGTTTGGTTACTTAGAAAGTAAATTATAGTGG
* * * * *
655324 AATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTTATTTAGGTGAAAAATTTAAATGTT
65 GATAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATT-AGTGTT
655389 CTTTTTGTTTTTTT
129 C-TTTTGTTTTTTT
655403 GGGTGTTTCT
Statistics
Matches: 698, Mismatches: 119, Indels: 68
0.79 0.13 0.08
Matches are distributed among these distances:
132 33 0.05
133 70 0.10
134 1 0.00
136 4 0.01
137 2 0.00
141 23 0.03
142 90 0.13
143 106 0.15
144 95 0.14
145 233 0.33
146 16 0.02
147 25 0.04
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (143 bp):
TGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
ATAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTAGTGTTCT
TTTGTTTTTTTTA
Found at i:654831 original size:278 final size:273
Alignment explanation
Indices: 654262--655238 Score: 1014
Period size: 278 Copynumber: 3.5 Consensus size: 273
654252 AATTTAGTGT
** * **
654262 TATTTTTGGTGGTTCTTTATGAATATAAGTATATTTTTTGTTGTTTGGTTACTTAGAAAGTAAAT
1 TATTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAAT
* * * *
654327 TTTAGT-GGATTAAGCTTAATTTAGCTACTTTAATCGTCTCAATTTCGTCATTTAGGTGAAAAAT
66 TATAGTGGGA-TAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA-
* * * ** *
654391 TTTAGTGTTCATTTTGGT-GGTTCTTTATGAATATAAGTATATAATTTGTTGTTGGGTTACTTAG
129 ---ATTGTTCA--TTAGTAAGTTCTTTATGAAT-TATCTATAT-ATTTGTTGTTTGGTTACTTAG
* * * * *
654455 AAAGTAAATTATAGTGGAATAAGCTTATGTTAGCTACTTTAATTTCTAAGTTTGGTCATTTAGGT
187 AAAGTAAATTATAGTGGGATAAGCTTAAGTTAGCTACTTTATTTTCTAAATTTCGTCATTTAGGT
*
654520 GAAAAACATTAGTGTTCTTCTGC
252 GAAAAA-ATTAGTGTTCTTATGC
* *
654543 TTTTTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAA
1 -TATTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAA
654608 TTATAGTGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA
65 TTATAGTGGGATAAGCTTAATTTA-ACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA
* *
654673 ATTGTT-ATTAGTAAGTTTCTTTATGAATTGATCTATATGTTTTGTTGTTTGGTTATTTAGAAAG
129 ATTGTTCATTAGTAAG-TTCTTTATGAATT-ATCTATAT-ATTTGTTGTTTGGTTACTTAGAAAG
** * * *
654737 TAAATGGTAGTGGGATAAGCTTAAG-AATGCTACTTTAGTTTTCTAAATTTCGTTACTTAGGTGA
191 TAAATTATAGTGGGATAAGCTTAAGTTA-GCTACTTTA-TTTTCTAAATTTCGTCATTTAGGTGA
*
654801 CAAAAGTTAGTGTTCTTATGC
254 -AAAAATTAGTGTTCTTATGC
* * * *
654822 TATTTTTTATGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGTAAAT
1 TATTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAAT
* * * * * *
654887 TACAGTGGGATAACCTTAATTTAGCTACTTTACTTTTCTAAATTTCTTCATTTAGGTGAAAAAAT
66 TATAGTGGGATAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAA-
* * *
654952 TTAGTGTCTTTTGTTTTTTTTTTATAGTTCTTTATGAA-TATCTTTATATTTGTTGTTTGGTTAC
130 TT-GT-TCATTAG---------TA-AGTTCTTTATGAATTATCTATATATTTGTTGTTTGGTTAC
* * * *
655016 TTAGAAAGTAAATTATAAT-GGATTGAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTCAT
183 TTAGAAAGTAAATTATAGTGGGA-TAAGCTTAAGTTAGCTAC-TTTATTTTCTAAATTTCGTCAT
** * * *
655080 TTAGGTGAAAACTTTTTGTGTTCTTTTGT
246 TTAGGTGAAAA-AATTAGTGTTCTTATGC
*** * * * * * *
655109 TA-TTAGCAAGTTTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAAT
1 TATTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAAT
* * *
655173 TGTAGTGGGATAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCGTTTAGGTAAAAAAAT
66 TATAGTGGGATAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAAT
655238 T
131 T
655239 TCGTGTTTCT
Statistics
Matches: 584, Mismatches: 85, Indels: 49
0.81 0.12 0.07
Matches are distributed among these distances:
276 4 0.01
277 40 0.07
278 153 0.26
279 42 0.07
280 5 0.01
281 3 0.01
282 76 0.13
283 40 0.07
285 2 0.00
286 110 0.19
287 81 0.14
288 12 0.02
289 1 0.00
290 13 0.02
291 2 0.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (273 bp):
TATTTTTTATGGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAAT
TATAGTGGGATAAGCTTAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAAT
TGTTCATTAGTAAGTTCTTTATGAATTATCTATATATTTGTTGTTTGGTTACTTAGAAAGTAAAT
TATAGTGGGATAAGCTTAAGTTAGCTACTTTATTTTCTAAATTTCGTCATTTAGGTGAAAAAATT
AGTGTTCTTATGC
Found at i:655229 original size:286 final size:287
Alignment explanation
Indices: 654838--655377 Score: 678
Period size: 286 Copynumber: 1.9 Consensus size: 287
654828 TTATGGTTCA
*
654838 TTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGATAACCT
1 TTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGCAAATTACAGTGGGATAACCT
* * * * *
654903 TAATTTAGCTACTTTACTTTTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTG--TCTTTTGT
66 TAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTAAAAAAATTTAGTGTTTCTTTTG-
* ** * ** * * * *
654966 TTTTTTTTTATAGTTCT-T-TATGAATATCTTTATAT-TTG-TTGTTTGGTTACTTAGAAAGTAA
130 -TTATTAGTA-AGTT-TATGCACAAACATATGTATATATTGCCT-TTTGGTTACTTAGAAAGTAA
* * * *
655027 ATTATAATGGATTGAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTCATTTAGGTGAAAAC
191 ATTATAATGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTCATTTAGGTGAAAAC
655092 TTTTTGTGTTCTTTTGTTATTAGCAAGTTTCT
256 TTTTTGTGTTCTTTTGTTATTAGCAAGTTTCT
* * * * * * ** *
655124 TTATGAATATGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGGATAAGCT
1 TTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGCAAATTACAGTGGGATAACCT
* *
655189 TAATTTAACTACTTTAATTGTCTAAATTTCGTCGTTTAGGTAAAAAAATTTCGTGTTTCTTTTGT
66 TAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTAAAAAAATTTAGTGTTTCTTTTGT
*
655254 TATTAGTAAGTTTATGCACAAACATATGTATATATTGCCTTTTGGTTGCTTAGAAAGTAAATTAT
131 TATTAGTAAGTTTATGCACAAACATATGTATATATTGCCTTTTGGTTACTTAGAAAGTAAATTAT
** *
655319 GGTGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTTATTTAGGTGAAAA
196 AATGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTCATTTAGGTGAAAA
655378 ATTTAAATGT
Statistics
Matches: 213, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
284 1 0.00
285 5 0.02
286 120 0.56
287 79 0.37
288 8 0.04
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (287 bp):
TTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGCAAATTACAGTGGGATAACCT
TAATTTAACTACTTTAATTGTCTAAATTTCGTCATTTAGGTAAAAAAATTTAGTGTTTCTTTTGT
TATTAGTAAGTTTATGCACAAACATATGTATATATTGCCTTTTGGTTACTTAGAAAGTAAATTAT
AATGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTCATTTAGGTGAAAACTTTTT
GTGTTCTTTTGTTATTAGCAAGTTTCT
Found at i:661412 original size:17 final size:17
Alignment explanation
Indices: 661390--661424 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
661380 ATAAAGAAGA
661390 AAAATATGCATATATAT
1 AAAATATGCATATATAT
*
661407 AAAATATGTATATATAT
1 AAAATATGCATATATAT
661424 A
1 A
661425 TATAGGCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
AAAATATGCATATATAT
Found at i:661780 original size:3 final size:3
Alignment explanation
Indices: 661772--661810 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
661762 ATATAAAAGC
* *
661772 AAT AAT AAT AAT AAT AAT AAT AGT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
661811 GTCAACTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:664407 original size:19 final size:20
Alignment explanation
Indices: 664367--664410 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
664357 GTCTCTTTAG
* *
664367 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
664386 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
664405 GCATTA
1 GCATTA
664411 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:667024 original size:19 final size:18
Alignment explanation
Indices: 667002--667049 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
666992 AGGGAAAAGG
667002 AAAAGAAAAAAACAAAATCA
1 AAAAGAAAAAAA-AAAAT-A
* *
667022 AAAGGAAAATAAAAAATA
1 AAAAGAAAAAAAAAAATA
667040 AAAAGAAAAA
1 AAAAGAAAAA
667050 GAGAAATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAATA
Found at i:667049 original size:25 final size:25
Alignment explanation
Indices: 666996--667055 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
666986 AAAACAAGGG
**
666996 AAAAGGAAAAGAAAAAAACAAAATC
1 AAAAGGAAAAGAAAAAAACAAAAGA
*
667021 AAAAGGAAAATAAAAAATA-AAAAGA
1 AAAAGGAAAAGAAAAAA-ACAAAAGA
667046 AAAAGAGAAA
1 AAAAG-GAAA
667056 TCAATCAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.05
Consensus pattern (25 bp):
AAAAGGAAAAGAAAAAAACAAAAGA
Found at i:668834 original size:44 final size:43
Alignment explanation
Indices: 668774--669012 Score: 162
Period size: 44 Copynumber: 5.4 Consensus size: 43
668764 GAAGCAGGTC
* *
668774 GAAGACATAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACAAAAATCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
* * * ** ** * * *
668817 GAAGACAAAAGATCTTGCCTTCCTAC-ATTGACAGCGAAGCAGATC
1 GAAGACAAAA-ATCTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTT
* * *
668862 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
1 GAAGACAAAAATCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
* ** * * *
668905 GAAGACAAAATATCTTG-CT-TTTCTGCATTG-GCAGCGAAGCAGATC
1 GAAGACAAAA-ATCTTGCCTCTTTC-G-GTTGTG-ATAG-AGCTGGTT
* *
668950 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACAAAAATCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
668993 GAAGACAAAAGATCTTGCCT
1 GAAGACAAAA-ATCTTGCCT
669013 TCCTACATTA
Statistics
Matches: 141, Mismatches: 42, Indels: 25
0.68 0.20 0.12
Matches are distributed among these distances:
42 4 0.03
43 45 0.32
44 52 0.37
45 36 0.26
46 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
GAAGACAAAAATCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
Found at i:668885 original size:88 final size:88
Alignment explanation
Indices: 668736--669259 Score: 684
Period size: 88 Copynumber: 6.0 Consensus size: 88
668726 CAATGAAGTT
* * * * *
668736 AAAGATCTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
668801 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
668824 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
*
668889 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* * * * *
668912 AAATATCTTGCTTTTCTGCATTGGCAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
668977 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
669000 AAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
* *
669065 TGTGATGGAGCTGGTTGAAGAAAA
66 TGTGATAGAGCTGGTTGAAG-ACA
* *
669089 AAAGATCTTGCTTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCTCTCGA
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTCTCG-
*
669152 G-TGTAGA-AGAGTTGGTTGAAGACA
64 GTTGT-GATAGAGCTGGTTGAAGACA
** * ** * * * *
669176 ACTGATTTTATCTTCCTGCGTTGACAGTGAAGCAGGTCGAAG--ACAAACCTTACCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
*
669239 TGT-AGTGGAGCTGGTTGAAGA
66 TGTGA-TAGAGCTGGTTGAAGA
669260 ATTGCAGATC
Statistics
Matches: 389, Mismatches: 39, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
84 1 0.00
85 1 0.00
86 29 0.07
87 43 0.11
88 271 0.70
89 44 0.11
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
TGTGATAGAGCTGGTTGAAGACA
Found at i:669054 original size:44 final size:44
Alignment explanation
Indices: 668830--669056 Score: 131
Period size: 44 Copynumber: 5.2 Consensus size: 44
668820 GACAAAAGAT
668830 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** * * * * *
668874 CTTGCC-TCTTTCGGTTGTGATG-G-AGCTGGTTGAAGACAAAATAT
1 CTTGCCTTCCTAC-ATTGACA-GCGAAGCAGATCGAAGACACAA-AC
* * * *
668918 CTTGCTTTTCTGCATTGGCAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
* * * ** ** * * * * *
668962 CTTGCC-TCTTTCGGTTGTGATAG-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTCCTAC-ATTGACAGCGAAGCAGATCGAAGACACAA-AC
*
669006 CTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
669050 CTTGCCT
1 CTTGCCT
669057 CTCTCGGTTG
Statistics
Matches: 124, Mismatches: 49, Indels: 20
0.64 0.25 0.10
Matches are distributed among these distances:
43 36 0.29
44 52 0.42
45 36 0.29
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (44 bp):
CTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAAC
Found at i:671031 original size:3 final size:3
Alignment explanation
Indices: 671023--671064 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
671013 TAAAGTTGAC
* *
671023 ATT ATT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
671065 GCTTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:671434 original size:15 final size:16
Alignment explanation
Indices: 671414--671446 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
671404 CGCCTATATA
671414 TATATATA-CATATTT
1 TATATATAGCATATTT
671429 TATATATATGCATATTT
1 TATATATA-GCATATTT
671446 T
1 T
671447 TCTTCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATAGCATATTT
Found at i:671434 original size:17 final size:17
Alignment explanation
Indices: 671412--671446 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
671402 TACGCCTATA
671412 TATATATATACATATTT
1 TATATATATACATATTT
*
671429 TATATATATGCATATTT
1 TATATATATACATATTT
671446 T
1 T
671447 TCTTCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (17 bp):
TATATATATACATATTT
Found at i:672785 original size:16 final size:16
Alignment explanation
Indices: 672760--672806 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
672750 ATTTAACTCC
*
672760 AAAAGTGGAAGAAACAA
1 AAAAGAGGAAGAAA-AA
672777 AAAAG-GGAAGAAAAA
1 AAAAGAGGAAGAAAAA
672792 AAAAGAAGGAAGAAA
1 AAAAG-AGGAAGAAA
672807 TGCTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.25
16 8 0.29
17 13 0.46
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (16 bp):
AAAAGAGGAAGAAAAA
Found at i:673324 original size:189 final size:178
Alignment explanation
Indices: 672977--673325 Score: 450
Period size: 189 Copynumber: 1.9 Consensus size: 178
672967 CTGTCTCTCC
*
672977 AAAACAGAGGATAAGCTCTCTCAAGGTCCCTCCTCCTCTTATATACACATTCATCATATCTACAT
1 AAAACAGAGGATAAGCTCTCTCAAGCTCCCTCCTCCTCTTATATA-ACATTCATCATATCTACAT
* *
673042 ACTTATACACATCACATAATACATAAGCATCATCATCCATATGTTCCATGTATCTTTGAGAAGTA
65 AATTATACACATCACATAATACATAAGCATCATCATCCATATGTTCCATGTATCTTTGAGAAGCA
*
673107 TACTCAAAGCTTGTAATCTGTTTCTTTTTTATTTTCTTGGGTTATATCA
130 TACCCAAAGCTTGTAATCTGTTTCTTTTTTATTTTCTTGGGTTATATCA
* * * **
673156 AAAACAGAGGATAAGCTTTCTCAAGCTCTCT-TTTTTCTTATAT-ACATTCATCATGTATACGTA
1 AAAACAGAGGATAAGCTCTCTCAAGCTCCCTCCTCCTCTTATATAACATTCATCA--TAT-C-TA
* *
673219 CATATATATATACACATCACATAATACATAAGCATCATCATCGTCCATTTGTTCTATGTATGCAT
62 CATA-AT-TATACACATCACATAATACATAAGCATCATCA---TCCATATGTTCCATGTAT-C-T
*
673284 GGTTTAGAAGCATACCCAAAGCTTGTAATCTGTTTCTTTTTT
120 --TTGAGAAGCATACCCAAAGCTTGTAATCTGTTTCTTTTTT
673326 TCTTTGTTTT
Statistics
Matches: 145, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
176 10 0.07
178 12 0.08
179 29 0.20
180 6 0.04
181 1 0.01
182 32 0.22
185 16 0.11
186 1 0.01
187 1 0.01
189 37 0.26
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (178 bp):
AAAACAGAGGATAAGCTCTCTCAAGCTCCCTCCTCCTCTTATATAACATTCATCATATCTACATA
ATTATACACATCACATAATACATAAGCATCATCATCCATATGTTCCATGTATCTTTGAGAAGCAT
ACCCAAAGCTTGTAATCTGTTTCTTTTTTATTTTCTTGGGTTATATCA
Found at i:673646 original size:4 final size:4
Alignment explanation
Indices: 673637--673670 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
673627 TTCCTCTTTT
673637 ATAC ATAC ATAC ATAC ATAC ATAC ATA- ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
673671 AGCATCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:673986 original size:30 final size:31
Alignment explanation
Indices: 673946--674004 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
673936 CAATACGGTG
673946 GGTACTCGAGCTCGGGTGTAAATATCGGAAA
1 GGTACTCGAGCTCGGGTGTAAATATCGGAAA
* *
673977 GGTAC-CGAGCTCGTGTGTAAATTTCGGA
1 GGTACTCGAGCTCGGGTGTAAATATCGGA
674005 TACAGGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (31 bp):
GGTACTCGAGCTCGGGTGTAAATATCGGAAA
Found at i:679736 original size:34 final size:34
Alignment explanation
Indices: 679698--679767 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
679688 AGATATCAAA
679698 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
1 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
679732 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
1 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
679766 AG
1 AG
679768 AAAACAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (34 bp):
AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
Found at i:680978 original size:33 final size:33
Alignment explanation
Indices: 680941--681006 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
680931 AATGTTACAA
680941 GATTTTACAAATTTACTTTTAAGTTAGTATACT
1 GATTTTACAAATTTACTTTTAAGTTAGTATACT
680974 GATTTTACAAATTTACTTTTAAGTTAGTATACT
1 GATTTTACAAATTTACTTTTAAGTTAGTATACT
681007 AGTTATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (33 bp):
GATTTTACAAATTTACTTTTAAGTTAGTATACT
Found at i:684152 original size:23 final size:23
Alignment explanation
Indices: 684126--684170 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
684116 CTAAAACCAT
684126 ATTA-TCCCTAAAAAATAGGTTTC
1 ATTATTCCCTAAAAAA-AGGTTTC
* *
684149 ATTATTCTCTATAAAAAGGTTT
1 ATTATTCCCTAAAAAAAGGTTT
684171 AATTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATTCCCTAAAAAAAGGTTTC
Found at i:684302 original size:30 final size:30
Alignment explanation
Indices: 684266--684338 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
684256 TTATAGTGTT
684266 AATTGTTCATATAAATAGTTAAGAATGGAC
1 AATTGTTCATATAAATAGTTAAGAATGGAC
684296 AATTGTTCATATAAATAGTTAAGAATGGAC
1 AATTGTTCATATAAATAGTTAAGAATGGAC
*
684326 AATTGTTCTTATA
1 AATTGTTCATATA
684339 GCTTCCTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (30 bp):
AATTGTTCATATAAATAGTTAAGAATGGAC
Found at i:685144 original size:6 final size:6
Alignment explanation
Indices: 685135--685164 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
685125 AGAAAATATA
685135 AAAATT AAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT
685165 TATGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:687014 original size:22 final size:22
Alignment explanation
Indices: 687002--687044 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
686992 TGCTGTTGTT
*
687002 TTGCTAATATTTTGTTATTATA
1 TTGCTAATATTTTGTTGTTATA
*
687024 TTGCTAATTTTTTGTTGTTAT
1 TTGCTAATATTTTGTTGTTAT
687045 TATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (22 bp):
TTGCTAATATTTTGTTGTTATA
Found at i:689305 original size:11 final size:11
Alignment explanation
Indices: 689289--689322 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
689279 TCTCATACAC
689289 AAAAAAAA-AA
1 AAAAAAAAGAA
*
689299 GAAAAAAAGAA
1 AAAAAAAAGAA
689310 AAAAAAAAGAA
1 AAAAAAAAGAA
689321 AA
1 AA
689323 CAGCAACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:691716 original size:15 final size:14
Alignment explanation
Indices: 691694--691724 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
691684 TAATATATTT
*
691694 GGAAAATTTTTAGA
1 GGAAAAATTTTAGA
691708 GGAAAAATTTTAGA
1 GGAAAAATTTTAGA
691722 GGA
1 GGA
691725 TCATATTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (14 bp):
GGAAAAATTTTAGA
Found at i:692852 original size:17 final size:18
Alignment explanation
Indices: 692827--692866 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
692817 ATTAATGTGG
*
692827 AAAAATGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
692844 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
692862 AAAAT
1 AAAAT
692867 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:696412 original size:15 final size:15
Alignment explanation
Indices: 696402--696431 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
696392 TCCCTTCTTG
696402 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
696417 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
696432 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:697198 original size:17 final size:18
Alignment explanation
Indices: 697173--697212 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
697163 CAAATTGTGG
*
697173 AAAAATGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
697190 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
697208 AAAAT
1 AAAAT
697213 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:703049 original size:7 final size:8
Alignment explanation
Indices: 703020--703046 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
703010 GATCCATTGA
703020 AAAATTAT
1 AAAATTAT
703028 AAAATTAT
1 AAAATTAT
703036 AAAATTAT
1 AAAATTAT
703044 AAA
1 AAA
703047 TTAGCCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Found at i:704595 original size:22 final size:22
Alignment explanation
Indices: 704570--704615 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
704560 ATAAATTTAT
704570 TAGTCAATTAAAATAGTTAAAA
1 TAGTCAATTAAAATAGTTAAAA
* ***
704592 TAGTTAATTATTCTAGTTAAAA
1 TAGTCAATTAAAATAGTTAAAA
704614 TA
1 TA
704616 TTGATGTGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
TAGTCAATTAAAATAGTTAAAA
Found at i:710550 original size:6 final size:6
Alignment explanation
Indices: 710539--710565 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
710529 AATCACTAAT
710539 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
710566 ACTGATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:711048 original size:43 final size:43
Alignment explanation
Indices: 711000--711102 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
710990 TTATTTAAAA
711000 AAACGCCGCTAAAGGTCCCGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCCCGACCTTTAGCGGCGCTTTTCCCAC
* **
711043 AAACGCCGCTAAAGATCGGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCCCGACCTTTAGCGGCGCTTTTCCCAC
711086 AAACGCCGCTAAAGGTC
1 AAACGCCGCTAAAGGTC
711103 ATAAAAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCCCGACCTTTAGCGGCGCTTTTCCCAC
Found at i:715015 original size:25 final size:25
Alignment explanation
Indices: 714981--715044 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
714971 TCTGTAAAAT
714981 CAATTGAAACGGTGCGTGGT-GGAAA
1 CAATTGAAACGGTGCGTGGTAGG-AA
715006 CAATTGAAACGGTGCGTGGTAGGAA
1 CAATTGAAACGGTGCGTGGTAGGAA
715031 CAATTGAAACGGTG
1 CAATTGAAACGGTG
715045 AGTTTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (25 bp):
CAATTGAAACGGTGCGTGGTAGGAA
Found at i:716207 original size:7 final size:7
Alignment explanation
Indices: 716195--716323 Score: 55
Period size: 7 Copynumber: 18.1 Consensus size: 7
716185 ACTAATTAAT
716195 CTAAACC
1 CTAAACC
716202 CTAAACC
1 CTAAACC
*
716209 TCTTAACTC
1 -CTAAAC-C
*
716218 CT-ATCC
1 CTAAACC
*
716224 CATAAACA
1 C-TAAACC
716232 CTAAACC
1 CTAAACC
716239 CTAAACC
1 CTAAACC
* *
716246 TTTAACC
1 CTAAACC
* *
716253 ATTAACC
1 CTAAACC
*
716260 CCAAACC
1 CTAAACC
*
716267 CTTACACC
1 C-TAAACC
*
716275 TTAAA-C
1 CTAAACC
* *
716281 TTTAACC
1 CTAAACC
*
716288 CTAACCC
1 CTAAACC
716295 CTAAACC
1 CTAAACC
* *
716302 TTAAATC
1 CTAAACC
* *
716309 ATAATCC
1 CTAAACC
716316 CTAAACC
1 CTAAACC
716323 C
1 C
716324 ATAATTCATC
Statistics
Matches: 89, Mismatches: 27, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
6 7 0.08
7 67 0.75
8 14 0.16
9 1 0.01
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:716265 original size:28 final size:28
Alignment explanation
Indices: 716234--716303 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
716224 CATAAACACT
*
716234 AAACCCTAAACCTTTAACCATTAACCCC
1 AAACCCTAAACCTTTAAACATTAACCCC
* * *
716262 AAACCCTTACACC-TTAAACTTTAACCCT
1 AAACCC-TAAACCTTTAAACATTAACCCC
*
716290 AACCCCTAAACCTT
1 AAACCCTAAACCTT
716304 AAATCATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.15
28 24 0.71
29 5 0.15
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACCCTAAACCTTTAAACATTAACCCC
Found at i:716392 original size:21 final size:21
Alignment explanation
Indices: 716366--716443 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
716356 ACTCTTAAAC
716366 CTTAAACCCTAAACCATATAT
1 CTTAAACCCTAAACCATATAT
* **
716387 CTTAAA-CC-ATA-GTTA-ACT
1 CTTAAACCCTAAACCATATA-T
*
716405 CATAAACCCTAAACCATATAT
1 CTTAAACCCTAAACCATATAT
* *
716426 ATTAAACCATAAACCATA
1 CTTAAACCCTAAACCATA
716444 AACTATAATG
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
17 1 0.02
18 8 0.19
19 4 0.10
20 4 0.10
21 24 0.57
22 1 0.02
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.27
Consensus pattern (21 bp):
CTTAAACCCTAAACCATATAT
Found at i:716653 original size:41 final size:41
Alignment explanation
Indices: 716608--716909 Score: 374
Period size: 41 Copynumber: 7.4 Consensus size: 41
716598 GTTATATGAC
*
716608 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* *
716649 TTTTAACGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* * * *
716690 TTTTAACTGTGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* * * * *
716731 TTTTAGCGACGCTTTGCCAAAAACGCCGCTAATACTCTGAT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* *
716772 TTTTAGCGGCGCTTTGCCAAAAGCGCCGCTAATGCTCTGAT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
*
716813 TTTTAGCAGCGTTTTTCCAAAAGCGCCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
* * ** * * *
716853 TTTTCGCGGCATTTTTGGTAAAAACGCTGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTT-CCAAAAGCGCCGCTAATGCTCTGAT
*
716894 TTTTAGTGGCGTTTTT
1 TTTTAGCGGCGTTTTT
716910 GGTAAAACGC
Statistics
Matches: 231, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 15 0.06
41 216 0.94
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGAT
Found at i:721999 original size:20 final size:19
Alignment explanation
Indices: 721962--722003 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
721952 ATTCATTCAC
721962 AAATAAAATAATAAAAAGCA
1 AAATAAAATAATAAAAAG-A
721982 AAATAAAATAA-AATAAAGA
1 AAATAAAATAATAA-AAAGA
722001 AAA
1 AAA
722004 CAAGAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (19 bp):
AAATAAAATAATAAAAAGA
Found at i:725369 original size:20 final size:20
Alignment explanation
Indices: 725346--725403 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
725336 AATTCAAGTT
725346 TTTTAATTTAATAAATATAA
1 TTTTAATTTAATAAATATAA
* *
725366 TTTTAAATATAA-AAATATGA
1 TTTT-AATTTAATAAATATAA
725386 TTTT-ATTT--TAAATATAA
1 TTTTAATTTAATAAATATAA
725403 T
1 T
725404 AAGTAGAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 8 0.25
18 3 0.09
20 15 0.47
21 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTAATTTAATAAATATAA
Found at i:729166 original size:237 final size:238
Alignment explanation
Indices: 728689--729223 Score: 735
Period size: 237 Copynumber: 2.3 Consensus size: 238
728679 ATAGTCCGAT
* * * *
728689 GGGGGAATATCAGGTTCATTTATAACAAACATGTCCAAAAGAGAAGCACATTAGAAGTATGTGTT
1 GGGGGAATATCGGGTTCATTTATACCAAACATATCCAAAAGAGAAGCACATTAGAAGTATGTGCT
* * * *
728754 AGATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTTGGAACATGTTTTTGTTGAAGCA
66 AGATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTAGAAACATGTTGTCGTTGAAGCA
* *
728819 TCACATCGAGTTTATTATCCATAGATTATAGCTTCTAAGAGTAATCACAGCAAATATCACATTTA
131 TCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAATCACAGCAAATATCACATTTA
728884 ACTAGAACCCACTTCGGATTACGAACATATTCAACAGTTTGAA
196 ACTAGAACCCACTTCGGATTACGAACATATTCAACAGTTTGAA
* * * *
728927 GGGGGAATATTGGGTTCATTTATTCCGAACATAT-CAGAAAGAGAAGTACATTAGAAGTATG-GC
1 GGGGGAATATCGGGTTCATTTATACCAAACATATCCA-AAAGAGAAGCACATTAGAAGTATGTGC
* * * *
728990 TAGAATCTTATAGCGG-CAAAGCCATGTCAATGAGCCTAGATGCTCAGAAACGTGTTGTCGTTGA
65 TAG-ATCTCATAACGGTC-AAGCCATGTCAACGAGCCTAGATGCT-AGAAACATGTTGTCGTTGA
* * *
729054 AGCA-C-CATCGAGTTTATTGTCCAT-GATCATACCTTCTAAGAGTAATTCACAGGAAATATCGC
127 AGCATCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAA-TCACAGCAAATATCAC
*
729116 ATTTAACTAGAACCCACTTCGGATTA-GTAACATATTCAACGGTTTGAA
191 ATTTAACTAGAACCCACTTCGGATTACG-AACATATTCAACAGTTTGAA
* *
729164 GGGGGAATATCGGGTTCTTTTATACCTAAA-ATATCCAAAAGATAAGCACATTAGAAGTAT
1 GGGGGAATATCGGGTTCATTTATACC-AAACATATCCAAAAGAGAAGCACATTAGAAGTAT
729224 AATGGTAAAG
Statistics
Matches: 261, Mismatches: 28, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
236 20 0.08
237 132 0.51
238 91 0.35
239 18 0.07
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (238 bp):
GGGGGAATATCGGGTTCATTTATACCAAACATATCCAAAAGAGAAGCACATTAGAAGTATGTGCT
AGATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTAGAAACATGTTGTCGTTGAAGCA
TCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAATCACAGCAAATATCACATTTA
ACTAGAACCCACTTCGGATTACGAACATATTCAACAGTTTGAA
Found at i:729915 original size:31 final size:31
Alignment explanation
Indices: 729880--729942 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
729870 AGATAGTTCC
729880 ACTAACAGATACTATGAAGACATATGTATAT
1 ACTAACAGATACTATGAAGACATATGTATAT
729911 ACTAACAGATACTATGAAGACATATGTATAT
1 ACTAACAGATACTATGAAGACATATGTATAT
729942 A
1 A
729943 GGCAATGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
ACTAACAGATACTATGAAGACATATGTATAT
Found at i:733198 original size:21 final size:22
Alignment explanation
Indices: 733169--733215 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
733159 CAGAAGGAGT
*
733169 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
733191 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
733212 GAGT
1 GAGT
733216 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:734094 original size:16 final size:16
Alignment explanation
Indices: 734073--734112 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
734063 CAGATACATG
734073 CATGCATACATCCATC
1 CATGCATACATCCATC
*
734089 CATGCATCCATCCATC
1 CATGCATACATCCATC
*
734105 CATACATA
1 CATGCATA
734113 TACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (16 bp):
CATGCATACATCCATC
Found at i:740284 original size:167 final size:166
Alignment explanation
Indices: 739998--740332 Score: 580
Period size: 167 Copynumber: 2.0 Consensus size: 166
739988 TACATAAACT
* *
739998 AGTGGGAACTGACGTACTAAAAAATAAATTGTGCCAAAAAATTAGAATATACTCATTTTCCTTTG
1 AGTGGGAACTGACATACTAAAAAACAAATTGTGCCAAAAAATTAGAATATACTCATTTTCCTTTG
* *
740063 ATATCATATATCTAAGTTTCATATGTTATTATTTCATATCCATATATGGTAAAATTATATTTTGG
66 ATATCATATATCCAAGTTTCATATGTTATTATTTCATATCCATATATAGTAAAATTATATTTTGG
740128 TCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
131 TCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
* *
740164 AGTGGGATCTGACATACTAAAAAACCAATTGTGCCAAAAAATTAGAATGATACTCATTTTCCTTT
1 AGTGGGAACTGACATACTAAAAAACAAATTGTGCCAAAAAATTAGAAT-ATACTCATTTTCCTTT
* *
740229 GATATCATATATCCAAGTTTCATATGTTATTATTTCATATCTATATATAGTAAAATTGTATTTTG
65 GATATCATATATCCAAGTTTCATATGTTATTATTTCATATCCATATATAGTAAAATTATATTTTG
*
740294 GTCCCTAAAAATAAAAAGGTTTCTATTTATTTTTTTC
130 GTCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
740331 AG
1 AG
740333 AAGTGATGAA
Statistics
Matches: 159, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
166 44 0.28
167 115 0.72
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (166 bp):
AGTGGGAACTGACATACTAAAAAACAAATTGTGCCAAAAAATTAGAATATACTCATTTTCCTTTG
ATATCATATATCCAAGTTTCATATGTTATTATTTCATATCCATATATAGTAAAATTATATTTTGG
TCCCTAAAAATAAAAAGATTTCTATTTATTTTTTTC
Found at i:742221 original size:16 final size:17
Alignment explanation
Indices: 742200--742232 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
742190 AAAACAATTA
742200 ATTTAATC-TAAACTTT
1 ATTTAATCTTAAACTTT
742216 ATTTAATCTTAAACTTT
1 ATTTAATCTTAAACTTT
742233 TAAGATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAATCTTAAACTTT
Found at i:748809 original size:96 final size:96
Alignment explanation
Indices: 748641--748843 Score: 230
Period size: 96 Copynumber: 2.1 Consensus size: 96
748631 GGTTTCACCT
* * * *
748641 CCTTCAAAAGCGGTGGTCTCGATGTTCGAAGCAACTGTGGAACTTAGAACATTGAGTTCATTATA
1 CCTTCAAAAGCGGTCGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGAGTTCATTATA
*
748706 AAAATTTTCATCCTGCGAGAAGAACTGATCA
66 AAAATTTTCATCCTGCGAGAAGAACTGACCA
* * * **
748737 CCTTCAAAAGCGG-CGACGTCGATGTTCGAAGCAACTGTAGAATTTAGAACGCT-ATTTTGGTTA
1 CCTTCAAAAGCGGTCGAC-TCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGA-GTTCATTA
* * * *
748800 TAAATATTTTCCTCCTGCGTGAAGAATTGACCA
64 TAAAAATTTTCATCCTGCGAGAAGAACTGACCA
* *
748833 ACTTCATAAGC
1 CCTTCAAAAGC
748844 AGTGGCGCCG
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
95 3 0.03
96 86 0.97
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (96 bp):
CCTTCAAAAGCGGTCGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGAGTTCATTATA
AAAATTTTCATCCTGCGAGAAGAACTGACCA
Found at i:761342 original size:102 final size:102
Alignment explanation
Indices: 761143--761335 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 102
761133 ATTTATTACG
* * * *
761143 AATTGAATGTAGACTTTTGATTTTTAGATTGAAAAATCAGTGATTATAAATTTTTAATTAGCTAA
1 AATTGAATGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAAATTTTTAATTAGCTAA
*
761208 TAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
66 CAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
* *
761245 AATTGAATGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTAT-CATTTGTTAATTAGCTA
1 AATTGAATGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAAATTT-TTAATTAGCTA
* *
761309 CCAATCAGAGTGTTAAGCAGATAATTT
65 ACAATCAGAGTGATAAGCAGATAATTT
761336 TGTTATTTGG
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 4 0.05
102 77 0.95
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (102 bp):
AATTGAATGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAAATTTTTAATTAGCTAA
CAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
Found at i:766192 original size:32 final size:32
Alignment explanation
Indices: 766147--766210 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
766137 TTTTAGGATT
766147 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
1 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
* *
766179 TTCTAGGGGAACTGGGAATCCTGAAATGGCTA
1 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
766211 AGGAAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (32 bp):
TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
Found at i:770795 original size:69 final size:69
Alignment explanation
Indices: 770684--770823 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
770674 CCGGAAGGTA
* ** *
770684 AACAAATTGAAAACTGAAATCGAAGTGTCACATTTTGCATGTACTAGGGTAAGATATGTTTTGAT
1 AACAAATCGAAAACCAAAATCGAAGTGTCACATTTTGCATGTACTAGGATAAGATATGTTTTGAT
770749 GAAT
66 GAAT
* ** *
770753 AACAAATCGAAAACCAAAATCGAATTGTCATTTTTTGCATGTACTAGGATGAGATATGTTTTGAT
1 AACAAATCGAAAACCAAAATCGAAGTGTCACATTTTGCATGTACTAGGATAAGATATGTTTTGAT
770818 GAAT
66 GAAT
770822 AA
1 AA
770824 TCTCTAGCGG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (69 bp):
AACAAATCGAAAACCAAAATCGAAGTGTCACATTTTGCATGTACTAGGATAAGATATGTTTTGAT
GAAT
Found at i:771894 original size:21 final size:21
Alignment explanation
Indices: 771870--771922 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
771860 GCATTCAGCT
*
771870 TACCCTCCACCACCTTCCGCA
1 TACCCTCCACCACCTTCCACA
771891 TACCCTCCACCACCTTCCACA
1 TACCCTCCACCACCTTCCACA
771912 TACCCTCCACC
1 TACCCTCCACC
771923 TCCGCCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.58, G:0.02, T:0.19
Consensus pattern (21 bp):
TACCCTCCACCACCTTCCACA
Found at i:772193 original size:25 final size:25
Alignment explanation
Indices: 772159--772208 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
772149 CCAAGGGTTT
*
772159 CACATGTCAACCAAATGCAAAAATG
1 CACATGTCAACCAAAAGCAAAAATG
*
772184 CACATGTCAACCAAAAGCTAAAATG
1 CACATGTCAACCAAAAGCAAAAATG
772209 AGAAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (25 bp):
CACATGTCAACCAAAAGCAAAAATG
Found at i:772439 original size:18 final size:18
Alignment explanation
Indices: 772416--772451 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
772406 TTGACCTAAG
772416 GCAGACTATTTATTATCC
1 GCAGACTATTTATTATCC
772434 GCAGACTATTTATTATCC
1 GCAGACTATTTATTATCC
772452 TAACTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
GCAGACTATTTATTATCC
Found at i:781165 original size:15 final size:14
Alignment explanation
Indices: 781145--781252 Score: 51
Period size: 15 Copynumber: 7.2 Consensus size: 14
781135 TTTATGGAAA
781145 ATCAAAGATATGAGT
1 ATCAAAGATATG-GT
* *
781160 ATCAAATA-ATGGAA
1 ATCAAAGATATGG-T
781174 AGTCAAAGATATGGGT
1 A-TCAAAGATAT-GGT
* *
781190 ATCAAATA-ATGGAA
1 ATCAAAGATATGG-T
781204 AGTCAAAGATATGGGT
1 A-TCAAAGATAT-GGT
* *
781220 ATCAAATAT-TGGAA
1 ATCAAAGATATGG-T
781234 AGTCAAAGATATGGGT
1 A-TCAAAGATAT-GGT
781250 ATC
1 ATC
781253 GAGATATTGG
Statistics
Matches: 69, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
13 5 0.07
14 9 0.13
15 41 0.59
16 8 0.12
17 6 0.09
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.25
Consensus pattern (14 bp):
ATCAAAGATATGGT
Found at i:781174 original size:30 final size:30
Alignment explanation
Indices: 781138--781252 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
781128 ATCCATATTT
* *
781138 ATGGAAAATCAAAGATATGAGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
781168 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
781198 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
781228 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
781253 GAGATATTGG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.24
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:783451 original size:14 final size:14
Alignment explanation
Indices: 783432--783461 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
783422 GCTATATTTG
783432 GGGCACTTAATTGT
1 GGGCACTTAATTGT
783446 GGGCACTTAATTGT
1 GGGCACTTAATTGT
783460 GG
1 GG
783462 ACGTTGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (14 bp):
GGGCACTTAATTGT
Found at i:791280 original size:188 final size:177
Alignment explanation
Indices: 791019--791546 Score: 482
Period size: 188 Copynumber: 2.9 Consensus size: 177
791009 ACAACGATGG
* * * * *
791019 CAATGACAACATAATGAAGCCTTGAGATTTAGGTAGTTTTCAGAGA-TTACCTTGTTTCGGGTTC
1 CAATGACAACATAATGAAGCCTTGGGATTTGGGTA-CTTT-A-AGATTTACCTGGTTTCGGATTC
* * * * *
791083 AAG-AAAGCACCAAAGCCAAAAGATGGGAATGAATATGGCAAACATAATCAAGTCCAATGAACCA
63 AAGCAAAGCACCATAGCCAAAACAAGGGAATGAATATGGCAAACATAATAAAGGCCAATGAA-CA
* * *
791147 AATT-GAAGCTAAAAGCTCAATATTAAATCAAAGAACCAAAAGGAACAACAACAACGA
127 AATTCGAAGCTAAAAGCTCAACATCAAACCAAAGAACC-AAA--AAC-A-AACAA--A
* *
791204 CGACTGCAACAACATAATGAAGCCTTGGGATTTGGGTACTTTAAGATTTACCTGGTTTTAGGATT
1 C-AATG--ACAACATAATGAAGCCTTGGGATTTGGGTACTTTAAGATTTACCTGG-TTTCGGATT
** * * * * *
791269 CAAGCAAAGCACCATAGCCAGGACAAGGGAAGGTAA-ATGGAAAACACAATAAAGGCCAGTGGAC
62 CAAGCAAAGCACCATAGCCAAAACAAGGGAATG-AATATGGCAAACATAATAAAGGCCAATGAAC
* * *
791333 AAATTCGAAGCTAAAAGGTCAACATCAAACCAAAGAAGCAAACACAAACAAA
126 AAATTCGAAGCTAAAAGCTCAACATCAAACCAAAGAACCAAAAACAAACAAA
* * * ***
791385 CAATG--GATATAATGAAGCCTTGGGATTTGAGTACTTCCGGATTTACCTGGGTTTCGGATTCAA
1 CAATGACAACATAATGAAGCCTTGGGATTTGGGTACTTTAAGATTTACCT-GGTTTCGGATTCAA
* * *
791448 GCAAAGCACCATAGCCAAAACAAGGAAATGAATATGGCAAACATAATAAATG----TGGACAAAT
65 GCAAAGCACCATAGCCAAAACAAGGGAATGAATATGGCAAACATAATAAAGGCCAATGAACAAAT
* * * * *
791509 TTGAAGCTACAAGGTCAACATCAAAGCAAAGAAGCAAA
130 TCGAAGCTAAAAGCTCAACATCAAACCAAAGAACCAAA
791547 TAGAACAACA
Statistics
Matches: 290, Mismatches: 43, Indels: 33
0.79 0.12 0.09
Matches are distributed among these distances:
172 44 0.15
175 2 0.01
176 90 0.31
177 2 0.01
180 3 0.01
181 2 0.01
183 5 0.02
184 1 0.00
185 6 0.02
186 11 0.04
187 23 0.08
188 99 0.34
189 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (177 bp):
CAATGACAACATAATGAAGCCTTGGGATTTGGGTACTTTAAGATTTACCTGGTTTCGGATTCAAG
CAAAGCACCATAGCCAAAACAAGGGAATGAATATGGCAAACATAATAAAGGCCAATGAACAAATT
CGAAGCTAAAAGCTCAACATCAAACCAAAGAACCAAAAACAAACAAA
Found at i:807019 original size:13 final size:12
Alignment explanation
Indices: 807001--807034 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
806991 ACATAAATTC
807001 AAACAAATAAGGA
1 AAACAAAT-AGGA
807014 AAACAAATAGGA
1 AAACAAATAGGA
807026 ACAACAAAT
1 A-AACAAAT
807035 TAAAAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (12 bp):
AAACAAATAGGA
Found at i:807902 original size:121 final size:117
Alignment explanation
Indices: 807759--808014 Score: 300
Period size: 117 Copynumber: 2.2 Consensus size: 117
807749 TTTATTTTTA
* *
807759 AGCTCAAGCTCGGCTTGAGATATAATC-AAGCTATTCGAGCAAGCTCAATTAAGCTCATTTATCT
1 AGCTCAAGCTCAGCTTGAGATATAATCGAA-C---T-GAGCAAGCTCAATTAAGCTCATTTATCA
* *
807823 ATTTTTGTACTCAATCTTGAACTTCAGCTCAATTAAGCTCATA-TGTATTAAATCTTG
61 ATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACT-TATTAAAGCTTG
** * * *
807880 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGCTCAAGCTCGATTCAGCTTATTTATCAATTTT
1 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGAGCAAGCTCAATTAAGCTCATTTATCAATTTT
* * * * * *
807945 TGTACTCTAGCTTGAGCTTTAGCTCGATTACGCTCGTACTTATTAAAGCTTG
66 TGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACTTATTAAAGCTTG
*
807997 AGCTCGAGCTCAGCTTGA
1 AGCTCAAGCTCAGCTTGA
808015 TAATTAAGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
117 86 0.74
118 2 0.02
121 27 0.23
122 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (117 bp):
AGCTCAAGCTCAGCTTGAGATATAATCGAACTGAGCAAGCTCAATTAAGCTCATTTATCAATTTT
TGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACTTATTAAAGCTTG
Found at i:807969 original size:117 final size:117
Alignment explanation
Indices: 807798--808014 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 117
807788 GCTATTCGAG
* *
807798 CAAGCTCAATTAAGCTCATTTATCTATTTTTGTACTCAATCTTGAACTTCAGCTCAATTAAGCTC
1 CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
*
807863 ATA-TGTATTAAATCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
66 ATACT-TATTAAAGCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
* * * * * * * *
807915 CAAGCTCGATTCAGCTTATTTATCAATTTTTGTACTCTAGCTTGAGCTTTAGCTCGATTACGCTC
1 CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
* *
807980 GTACTTATTAAAGCTTGAGCTCGAGCTCAGCTTGA
66 ATACTTATTAAAGCTTGAGCTCAAGCTCAGCTTGA
808015 TAATTAAGCT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 85 0.99
118 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (117 bp):
CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
ATACTTATTAAAGCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
Found at i:808948 original size:11 final size:11
Alignment explanation
Indices: 808932--808959 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
808922 TTTGATCATT
808932 TAATTATAAAA
1 TAATTATAAAA
808943 TAATTATAAAA
1 TAATTATAAAA
808954 TAATTA
1 TAATTA
808960 CTTAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATTATAAAA
Found at i:812373 original size:22 final size:22
Alignment explanation
Indices: 812339--812380 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
812329 ACTATGATTT
*
812339 TTTTAATTATTTTAATTTATTA
1 TTTTAATTATTTTAAATTATTA
* *
812361 TTTTATTTCTTTTAAATTAT
1 TTTTAATTATTTTAAATTAT
812381 AATAGGAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTAATTATTTTAAATTATTA
Found at i:812510 original size:21 final size:20
Alignment explanation
Indices: 812486--812523 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
812476 ATTAAGCTTT
*
812486 TTATTTTTTTGAATATTTTAA
1 TTATATTTTT-AATATTTTAA
812507 TTATATTTTTAAT-TTTT
1 TTATATTTTTAATATTTT
812524 TTGAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 3 0.19
21 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTATATTTTTAATATTTTAA
Found at i:816359 original size:44 final size:44
Alignment explanation
Indices: 816311--816398 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
816301 ATTGTGTTCT
816311 GGGAAAGCAAAAGAGAGTGAAATTCGGTACTGCTATCCATAATA
1 GGGAAAGCAAAAGAGAGTGAAATTCGGTACTGCTATCCATAATA
816355 GGGAAAGCAAAAGAGAGTGAAATTCGGTACTGCTATCCATAATA
1 GGGAAAGCAAAAGAGAGTGAAATTCGGTACTGCTATCCATAATA
816399 CAAAAGGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (44 bp):
GGGAAAGCAAAAGAGAGTGAAATTCGGTACTGCTATCCATAATA
Found at i:829123 original size:21 final size:21
Alignment explanation
Indices: 829097--829137 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
829087 AGACAAGCAA
* *
829097 TACTCCATAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
829118 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
829138 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:832268 original size:19 final size:18
Alignment explanation
Indices: 832232--832271 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
832222 TTTAAAAAAA
* *
832232 TATAAATTTTAGATTTTT
1 TATAAATTTTAAAATTTT
832250 TATAAATATTTAAAATTTT
1 TATAAAT-TTTAAAATTTT
832269 TAT
1 TAT
832272 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATAAATTTTAAAATTTT
Found at i:835011 original size:31 final size:31
Alignment explanation
Indices: 834945--835011 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
834935 GTCATCGAAC
* *
834945 TATTAGAAAATTTTCATTTAAGTTATTGAAT
1 TATTAGAAAATTTTCATTTAAGTTACTGAAA
* * *
834976 TATTAGAGAGTTTTTATTTAAGTTACT-AAGA
1 TATTAGAAAATTTTCATTTAAGTTACTGAA-A
835007 TATTA
1 TATTA
835012 TGTTTTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (31 bp):
TATTAGAAAATTTTCATTTAAGTTACTGAAA
Found at i:854258 original size:16 final size:17
Alignment explanation
Indices: 854245--854282 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
854235 TTTATTTTTG
854245 AATTTATATATTTTAGA
1 AATTTATATATTTTAGA
854262 AATTTATATATTTTA-A
1 AATTTATATATTTTAGA
854278 AATTT
1 AATTT
854283 TCAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTATATATTTTAGA
Found at i:855558 original size:20 final size:21
Alignment explanation
Indices: 855535--855574 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
855525 CGTGAAATTG
855535 CCTTTATT-ATTATT-ATTAAA
1 CCTTT-TTAATTATTAATTAAA
855555 CCTTTTTAATTATTAATTAA
1 CCTTTTTAATTATTAATTAA
855575 TCTTTGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.61
21 5 0.28
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
CCTTTTTAATTATTAATTAAA
Found at i:863209 original size:132 final size:130
Alignment explanation
Indices: 862971--863360 Score: 561
Period size: 132 Copynumber: 3.0 Consensus size: 130
862961 AATTGCTTTC
862971 CCTGTATGTCACGAATTTGGGTTTTATGTGTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
1 CCTGTATGTCACGAATTTGGGTTTTA--TGTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* ** *
863036 TCGTCCTATCTTGTATCAAGAATCATAGACTTAGGATGTCTTTATACTGCTTATATCGGTTAATA
64 TCGTCCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTAATA
863101 TA
129 TA
*
863103 TCTGTATGTCACGAATTTGGGTTTTATCCGTTCTTTTACCTGACTGCTAACTC-TAATCATTTTG
1 CCTGTATGTCACGAATTTGGGTTTTAT--GTTCTTTTACCTGACTGCTAACTCAT-ATCATTTTG
* *
863167 CTCATGCC-ATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGATTATATCGGTTAA
63 CTCGT-CCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTAA
863231 TATA
127 TATA
*
863235 CCTATATGTCACGAATCTT-GGTTTTATGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
1 CCTGTATGTCACGAAT-TTGGGTTTTATG-TTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* * * * * *
863299 TCGTCCTGTTTCGTATTAAGAATCATAGACTGCAGATGTCTTTGTACTGCATATATCTGTTA
64 TCGTCCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTA
863361 TCCAAAAACT
Statistics
Matches: 233, Mismatches: 17, Indels: 17
0.87 0.06 0.06
Matches are distributed among these distances:
130 4 0.02
131 85 0.36
132 140 0.60
133 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (130 bp):
CCTGTATGTCACGAATTTGGGTTTTATGTTCTTTTACCTGACTGCTAACTCATATCATTTTGCTC
GTCCTATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTAATATA
Found at i:867118 original size:18 final size:18
Alignment explanation
Indices: 867095--867129 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
867085 AGTCAAAAAA
867095 ACAAATCAAACTTTTCTC
1 ACAAATCAAACTTTTCTC
867113 ACAAATCAAACTTTTCT
1 ACAAATCAAACTTTTCT
867130 AAGTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (18 bp):
ACAAATCAAACTTTTCTC
Found at i:874176 original size:171 final size:171
Alignment explanation
Indices: 873877--874195 Score: 539
Period size: 171 Copynumber: 1.9 Consensus size: 171
873867 AAAGCACCAA
**
873877 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTCCCTTTGGACAAGAAAAT
1 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
* * *
873942 GACCTTCGGGCATAATCTTGGAGTCAAGGTGGCTTCTAAAGTTAACGGTGAAAAATACACCATGA
66 GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
874007 TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
131 TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
* * * *
874048 AAAGTTTGAACTTTGAACATGACAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAACAT
1 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
*
874113 GACCTTCAGGCCTAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
66 GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
*
874178 TGAGAGCACTAAAATGTA
131 TAAGAGCACTAAAATGTA
874196 TTATGCTGCT
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 137 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (171 bp):
AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
Found at i:877214 original size:14 final size:14
Alignment explanation
Indices: 877195--877223 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
877185 GGTTATTCTG
877195 TCAGCCACTTTAGA
1 TCAGCCACTTTAGA
877209 TCAGCCACTTTAGA
1 TCAGCCACTTTAGA
877223 T
1 T
877224 AAAAGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (14 bp):
TCAGCCACTTTAGA
Found at i:879206 original size:14 final size:14
Alignment explanation
Indices: 879184--879217 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
879174 GCCGTTTCGC
*
879184 TATTATATTGTTAT
1 TATTTTATTGTTAT
879198 TATTTTATTGTTAT
1 TATTTTATTGTTAT
*
879212 TGTTTT
1 TATTTT
879218 GATATTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:879645 original size:20 final size:20
Alignment explanation
Indices: 879612--879651 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
879602 ATATATTTAC
*
879612 TATATATTATAAAATATAAA
1 TATATATTAAAAAATATAAA
* *
879632 TATATTTTAAAAAATTTAAA
1 TATATATTAAAAAATATAAA
879652 AAATATGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATATTAAAAAATATAAA
Found at i:884299 original size:13 final size:13
Alignment explanation
Indices: 884281--884344 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
884271 AATTCTTCAT
*
884281 TGCTTTTGAAATG
1 TGCTTTTGAAAAG
*
884294 TGCTTTAGAAAAG
1 TGCTTTTGAAAAG
*
884307 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
884320 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
884333 TGCTTTAGAAAA
1 TGCTTTTGAAAA
884345 ATTTAAGTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.05
13 36 0.88
14 3 0.07
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:892433 original size:57 final size:57
Alignment explanation
Indices: 892365--892531 Score: 298
Period size: 57 Copynumber: 2.9 Consensus size: 57
892355 CGGACATAAG
892365 GAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTCC
1 GAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTCC
* *
892422 GAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTTCTACAACAAATTGGATTGCTCC
1 GAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTCC
* *
892479 GAGTTCTGGGGATGCCTCCTCATCCTCGTTTTGTCCAACCACAAATTGGATTG
1 GAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTG
892532 AGAGCAACAA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 104 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (57 bp):
GAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTCC
Found at i:904667 original size:46 final size:46
Alignment explanation
Indices: 904483--904676 Score: 132
Period size: 46 Copynumber: 4.3 Consensus size: 46
904473 ATCCGCTTCG
*
904483 CTGCCAAAAACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
* ** * * ** * *
904529 CTGCCAGATACA-GAGAGATAGAGTTAT-C-GGCTTCAATGTACTCCA
1 CTGCCAAATACAGGA-AGGCA-AGATCTGCAATCTTCAATCTATTCCA
* * * * * * * * *
904574 CTG--TAGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CG
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT-ATTCCA
904617 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
*
904663 CTGCCAGATACAGG
1 CTGCCAAATACAGG
904677 GAGATAGAGT
Statistics
Matches: 103, Mismatches: 35, Indels: 20
0.65 0.22 0.13
Matches are distributed among these distances:
41 3 0.03
42 7 0.07
43 13 0.13
44 1 0.01
45 22 0.21
46 53 0.51
47 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
Found at i:916092 original size:8 final size:9
Alignment explanation
Indices: 916071--916109 Score: 55
Period size: 8 Copynumber: 4.4 Consensus size: 9
916061 TCCTCTTAAA
916071 ATTTAAATTT
1 ATTTAAA-TT
916081 ATTT-AATT
1 ATTTAAATT
916089 ATTTAAATT
1 ATTTAAATT
916098 -TTTAAATT
1 ATTTAAATT
916106 ATTT
1 ATTT
916110 TTTACTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 14 0.52
9 9 0.33
10 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTAAATT
Found at i:916105 original size:17 final size:18
Alignment explanation
Indices: 916071--916109 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
916061 TCCTCTTAAA
*
916071 ATTTAAATTTATTTAATT
1 ATTTAAATTTATTAAATT
916089 ATTTAAATTT-TTAAATT
1 ATTTAAATTTATTAAATT
916106 ATTT
1 ATTT
916110 TTTACTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAAATTTATTAAATT
Found at i:916686 original size:35 final size:35
Alignment explanation
Indices: 916647--916715 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
916637 CATTAAATAC
916647 CAAAGTTTCCTCACTAATCATCGATTGAGTCTTAT
1 CAAAGTTTCCTCACTAATCATCGATTGAGTCTTAT
916682 CAAAGTTTCCTCACTAATCATCGATTGAGTCTTA
1 CAAAGTTTCCTCACTAATCATCGATTGAGTCTTA
916716 ACTCGATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (35 bp):
CAAAGTTTCCTCACTAATCATCGATTGAGTCTTAT
Found at i:941412 original size:8 final size:7
Alignment explanation
Indices: 941395--941429 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
941385 AAATATAAAA
*
941395 TTTTAAT
1 TTTTTAT
941402 TTTTTAT
1 TTTTTAT
941409 TTTTTAT
1 TTTTTAT
941416 TTTTTAT
1 TTTTTAT
*
941423 TATTTAT
1 TTTTTAT
941430 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:948265 original size:21 final size:22
Alignment explanation
Indices: 948227--948268 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
948217 TTCACCCCAT
948227 ATGGCATTTTGCTTTACTTCCG
1 ATGGCATTTTGCTTTACTTCCG
948249 ATGGC-TTTT-CTTCTACTTCC
1 ATGGCATTTTGCTT-TACTTCC
948269 AGTGAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGGCATTTTGCTTTACTTCCG
Found at i:949924 original size:378 final size:375
Alignment explanation
Indices: 949146--950038 Score: 1100
Period size: 378 Copynumber: 2.4 Consensus size: 375
949136 AAATTTAATG
* * * *
949146 AAGGCAAAATTTGAATTACAAA-TTTCTAGGAGGGGTCAAAAATGCAATTTCACCGTTTTATCCA
1 AAGGCAAAATCTAAATTACAAATTTTC-AGGAGGGGTCAAAAATGAAATTTCACCATTTTAT-CA
* * *
949210 AGGTGCCAAATCCAAAGCCTCTAG-TCCCTTTGGATTGGCCCTTTCTCTATCCTATTTTTT-TAC
64 TGGTGCCAAATCCAAAGCCTCTAGCT-CCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTGT-T
* * * *
949273 CGA-CTGTTTTCGGACATGGCGTATGAGATATGATCGGTCAAATTTGATCTTGGTCCTTCTTATT
127 TGACCTGTTTTGGGACATGGCGTATGAGATATGATCAGTCAAATTCGATCTTGGTCCTTCTTATT
* * * * * *
949337 ATACTTAAATTTGATTTTTAGTCTTTATACTTTAATTTGATATTATTGGTTTTTCTTCTTTTATA
192 ATACTAAAATTTGATATTTAGTCTTTATAATTTAATTTGATATAATTGATTTTTCTACTTTTATA
* * * **
949402 ATATCATTTGTCGGTTCAAATCATTAATTATTTTGATTAAAACATTATGATAAATATTCTTTTGG
257 ATATCATTGGTCAGTTCAAATCATTAACTATTCCGATTAAAACATTATGATAAATATTCTTTTGG
* * **
949467 GAATCGAGGTAAAAATATAAATTAAACTGGCTGAAGCTAAAAATTTAATGTTAA
322 GAATCAAGGTAAAAATATAAATTAAACTGACCAAAGCTAAAAATTTAATGTTAA
* *
949521 AAGGCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTATGTAT
1 AAGGCAAAATCTAAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTAT-CAT
* * * *
949586 CGTACCAAATCCGAAGCTTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTGTTTGA
65 GGTGCCAAATCCAAAGCCTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTGTTTGA
* * * *
949651 CCTGTTTTGGGACGTGGGGTATGAGATATGATCAGTCAAATTACGGTCTTGGTCCTTCTTATTGT
130 CCTGTTTTGGGACATGGCGTATGAGATATGATCAGTCAAATT-CGATCTTGGTCCTTCTTATTAT
*
949716 ACTAAAATTTGATATTTAGTCTTTATAATTTATTTTGATATAATTTGATCTTTT-TACTTTTATA
194 ACTAAAATTTGATATTTAGTCTTTATAATTTAATTTGATATAA-TTGAT-TTTTCTACTTTTATA
** * * *
949780 ATATTGTTGGTTAGTTCAAATCATTACCTATTCCGGTTAAAACATTATGATAAATATT-TTATTG
257 ATATCATTGGTCAGTTCAAATCATTAACTATTCCGATTAAAACATTATGATAAATATTCTT-TTG
* * *
949844 GGAATCAAGGTAAATATATATATTCAACTGACCAAAGCTAAAAATTTAATGTTAA
321 GGAATCAAGGTAAAAATATAAATTAAACTGACCAAAGCTAAAAATTTAATGTTAA
* * * * * * * *
949899 AAGGTAAAA-CTTAAATTATAAATTTTTAGAAGGGGCCAAAAATGAAATTTAACTATTTTATCCT
1 AAGGCAAAATC-TAAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTATCAT
** * * *
949963 GGTGCCAAATCCAAAGCCAGTAGCCCCTTTGGGTTGGTCCTTTCTCTATACTA-TTTTTGTTTGA
65 GGTGCCAAATCCAAAGCCTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTGTTTGA
*
950027 CCTATTTCTGGG
130 CCTGTTT-TGGG
950039 CATTGTTCAC
Statistics
Matches: 444, Mismatches: 64, Indels: 18
0.84 0.12 0.03
Matches are distributed among these distances:
375 108 0.24
376 60 0.14
377 109 0.25
378 163 0.37
379 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40
Consensus pattern (375 bp):
AAGGCAAAATCTAAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTTCACCATTTTATCATG
GTGCCAAATCCAAAGCCTCTAGCTCCTTTGGGTTGGCCCTTTCTCTATCCTATTTTTTGTTTGAC
CTGTTTTGGGACATGGCGTATGAGATATGATCAGTCAAATTCGATCTTGGTCCTTCTTATTATAC
TAAAATTTGATATTTAGTCTTTATAATTTAATTTGATATAATTGATTTTTCTACTTTTATAATAT
CATTGGTCAGTTCAAATCATTAACTATTCCGATTAAAACATTATGATAAATATTCTTTTGGGAAT
CAAGGTAAAAATATAAATTAAACTGACCAAAGCTAAAAATTTAATGTTAA
Found at i:950103 original size:14 final size:14
Alignment explanation
Indices: 950080--950119 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
950070 TTAATGACAT
950080 TATAAAATTAAAAA
1 TATAAAATTAAAAA
*
950094 TATCAAATT-AAAA
1 TATAAAATTAAAAA
950107 TATAAAGATTAAA
1 TATAAA-ATTAAA
950120 TCATCGGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 11 0.50
15 2 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (14 bp):
TATAAAATTAAAAA
Found at i:950516 original size:18 final size:17
Alignment explanation
Indices: 950493--950528 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
950483 TGCTAACTAC
*
950493 AATTATATTCATATATTA
1 AATTATAATCATA-ATTA
950511 AATTATAATCATAATTA
1 AATTATAATCATAATTA
950528 A
1 A
950529 TGACTGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATAATCATAATTA
Found at i:952655 original size:27 final size:26
Alignment explanation
Indices: 952600--952656 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
952590 AAATTTATTT
* * *
952600 AATTTATTTTAAAAAATTAATGGTCA
1 AATTTATTTTAAAAAATAAATGATAA
952626 AATTTATCTTTAAAAAAATAAAT-ATAA
1 AATTTAT-TTT-AAAAAATAAATGATAA
952653 AATT
1 AATT
952657 AACAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 9 0.35
28 10 0.38
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
AATTTATTTTAAAAAATAAATGATAA
Found at i:959330 original size:30 final size:31
Alignment explanation
Indices: 959295--959358 Score: 121
Period size: 30 Copynumber: 2.1 Consensus size: 31
959285 TATAAAATTA
959295 TAATTAATAGGAACATTT-AAAAAAATAAAT
1 TAATTAATAGGAACATTTAAAAAAAATAAAT
959325 TAATTAATAGGAACATTTAAAAAAAATAAAT
1 TAATTAATAGGAACATTTAAAAAAAATAAAT
959356 TAA
1 TAA
959359 CTCCTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (31 bp):
TAATTAATAGGAACATTTAAAAAAAATAAAT
Found at i:970871 original size:19 final size:20
Alignment explanation
Indices: 970829--970880 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
970819 CTTAACAAAA
*
970829 AAAAAATCAAAATAGTTTTC
1 AAAAATTCAAAATAGTTTTC
970849 AAAAATTCAAAATA-TTTAT-
1 AAAAATTCAAAATAGTTT-TC
*
970868 AAAAATTAAAAAT
1 AAAAATTCAAAAT
970881 TCTAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATTCAAAATAGTTTTC
Found at i:985700 original size:78 final size:78
Alignment explanation
Indices: 985612--985846 Score: 371
Period size: 78 Copynumber: 3.0 Consensus size: 78
985602 GTCAGGCAGA
* **
985612 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
985677 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
*
985690 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
985755 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
* * * * * *
985768 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCATAATCAAGCTACTGAGTCGGAAGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
*
985833 CAGCTTTCTGGAC
66 CGGCTTTCTGGAC
985846 G
1 G
985847 GCATGTCCGT
Statistics
Matches: 144, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 144 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (78 bp):
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC
Found at i:986953 original size:192 final size:189
Alignment explanation
Indices: 986626--987001 Score: 524
Period size: 192 Copynumber: 2.0 Consensus size: 189
986616 AGTTTTTTGG
*
986626 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATTTTCACTGA
1 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
* * * *
986691 TATTCTGTCAATTTTGGGCTGGTATTGCAATTTGACTTGCCATTTTTGCTTGCATTGTGGTTTTA
66 TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
* **
986756 TTATTTGGGGTTGTGCCGTAGTTTAATTTCCATACCATAGTAAAAAGCTTCTTTATTGTAGC
131 TTATTT--AGTCATGCCGTAGTTTAATTTCCATACCATAGT-AAAAGCTTCTTTATTGTAGC
*
986818 AATTAAAAAGATGTT-GG-TTATTGTTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACT
1 AATT-AAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGG-TTTTATATTCACT
* * * * *
986881 GATATTCTGTCTATTTCGATCTGGTATTGCATTTTGAATTGCTACTTTTGCTTG-TTTCGTGGTT
64 GATATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATT-GTGGTT
* * *
986945 TTATTATTTAGTCATGCCGTAGTTTATTTTCCATTCCATAGTAGAAGCTTCTTTATT
128 TTATTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATT
987002 ATATATAATC
Statistics
Matches: 164, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
189 14 0.09
190 28 0.17
191 33 0.20
192 79 0.48
193 10 0.06
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47
Consensus pattern (189 bp):
AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
TTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATTGTAGC
Found at i:988442 original size:31 final size:31
Alignment explanation
Indices: 988407--988476 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
988397 TGCAAAATTT
* *
988407 TTATTGAGTTTTTTGAAAGTTTTCA-TTTAAA
1 TTATTGAGTTATTTGAAAGTTAT-ATTTTAAA
* *
988438 TTATTGAATTATTTGAAAGTTATATTTTAAG
1 TTATTGAGTTATTTGAAAGTTATATTTTAAA
988469 TTATTGAG
1 TTATTGAG
988477 CTGTTAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.53
Consensus pattern (31 bp):
TTATTGAGTTATTTGAAAGTTATATTTTAAA
Found at i:988867 original size:41 final size:41
Alignment explanation
Indices: 988821--988946 Score: 194
Period size: 35 Copynumber: 3.2 Consensus size: 41
988811 ACTAAATCAT
*
988821 AATATCTCATATAATACACTTAGATTTGTATGCTTCTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
988862 AATATCTC-----ATA-ACTTAGATTTGTATGCTTGTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
988897 AATATCTCATATAATACACTTAGATTTGTATGCTTGT-ATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
988937 AATATCTCAT
1 AATATCTCAT
988947 TTAGTAAGAA
Statistics
Matches: 78, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
35 31 0.40
36 3 0.04
40 16 0.21
41 28 0.36
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (41 bp):
AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
Found at i:991556 original size:55 final size:55
Alignment explanation
Indices: 991472--991582 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
991462 ACGTATATCT
*
991472 CCTATTGATGTATAAAAACTAGTTTTTCAATTGTAGAAATTGATAGAATTTTTAA
1 CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAGAAATTGATAGAATTTTTAA
991527 CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAGAAATTGATAGAATTTTTAA
1 CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAGAAATTGATAGAATTTTTAA
991582 C
1 C
991583 GAAGAATTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (55 bp):
CCTATTGATGTATAAAAACTAGTTTTTCAACTGTAGAAATTGATAGAATTTTTAA
Found at i:996868 original size:123 final size:123
Alignment explanation
Indices: 996708--996936 Score: 336
Period size: 123 Copynumber: 1.9 Consensus size: 123
996698 TTTGCCTCAT
* * * *
996708 CTGGATTGTTGATGAAATTTGGGTTTGAAACTAAAAGCTTATTCGAGTTAGTAAGCGAAAGGTTC
1 CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATTCGAGTTAGTAAGCGAAAGGTTC
*
996773 AAGTCC-TTTCCATTCGTGTTTTAGCTT-TGTTCATCTTGTTTTTCCTCATATGGATTGC
66 AAGTCCTTTTCCATT-GTGTTGTAG-TTCTGTTCATCTTGTTTTTCCTCATATGGATTGC
* **
996831 CTGGATTGTTGACGAAATTCGGGTTTGAAACCGAAAGCTCATTCGAGTTAGTAATTGAAAGGTTC
1 CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATTCGAGTTAGTAAGCGAAAGGTTC
**
996896 AAGTCCTTTTTGATTGTGTTGTAGTTCTGTTCATCTTGTTT
66 AAGTCCTTTTCCATTGTGTTGTAGTTCTGTTCATCTTGTTT
996937 AGATTGCTGT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
122 2 0.02
123 86 0.91
124 6 0.06
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (123 bp):
CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATTCGAGTTAGTAAGCGAAAGGTTC
AAGTCCTTTTCCATTGTGTTGTAGTTCTGTTCATCTTGTTTTTCCTCATATGGATTGC
Found at i:1000728 original size:6 final size:6
Alignment explanation
Indices: 1000687--1000728 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1000677 GAGTAGTAGT
* *
1000687 AGGAGT AGGAGC AGGAGC AGGTGC AGGAGC AGGAGC AGGAGC
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
1000729 TGCTGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.31, C:0.14, G:0.50, T:0.05
Consensus pattern (6 bp):
AGGAGC
Found at i:1006439 original size:31 final size:31
Alignment explanation
Indices: 1006404--1006471 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1006394 GTGAAAACTT
1006404 AATGACTTAAATAAAAAAATTCAAATAGTTC
1 AATGACTTAAATAAAAAAATTCAAATAGTTC
* ** * *
1006435 AATGACTTAAATGAAAACTTTTAAATAGTTT
1 AATGACTTAAATAAAAAAATTCAAATAGTTC
1006466 AATGAC
1 AATGAC
1006472 CATGTTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (31 bp):
AATGACTTAAATAAAAAAATTCAAATAGTTC
Found at i:1010057 original size:13 final size:13
Alignment explanation
Indices: 1010039--1010063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010029 TTGGGCAAAA
1010039 CAAAAATCAAGTT
1 CAAAAATCAAGTT
1010052 CAAAAATCAAGT
1 CAAAAATCAAGT
1010064 CCAATTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
CAAAAATCAAGTT
Found at i:1026574 original size:41 final size:41
Alignment explanation
Indices: 1026528--1026613 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
1026518 GTTGAATTGC
1026528 TAATATTATTATGTTTGAATTTTTCATGATTTTATTAATAG
1 TAATATTATTATGTTTGAATTTTTCATGATTTTATTAATAG
*
1026569 TAATATTATTATGTTTGAATTTTTTATGATTTTATTAATAG
1 TAATATTATTATGTTTGAATTTTTCATGATTTTATTAATAG
1026610 -AATA
1 TAATA
1026614 AATTTAGTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (41 bp):
TAATATTATTATGTTTGAATTTTTCATGATTTTATTAATAG
Found at i:1026919 original size:18 final size:17
Alignment explanation
Indices: 1026898--1026955 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
1026888 AAAATATTAA
1026898 AAATATATTTTTAGAATT
1 AAATATATTTTTA-AATT
**
1026916 AAAT-TAATTTTTAAAAA
1 AAATAT-ATTTTTAAATT
1026933 AAATTATATTATTTAAATT
1 AAA-TATATT-TTTAAATT
1026952 AAAT
1 AAAT
1026956 TCAGACGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.19
18 16 0.50
19 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
AAATATATTTTTAAATT
Found at i:1026955 original size:19 final size:18
Alignment explanation
Indices: 1026901--1026956 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
1026891 ATATTAAAAA
1026901 TATATTTTTAGAATTAAAT
1 TATATTTTTA-AATTAAAT
**
1026920 TA-ATTTTTAAAAAAAAT
1 TATATTTTTAAATTAAAT
1026937 TATATTATTTAAATTAAAT
1 TATATT-TTTAAATTAAAT
1026956 T
1 T
1026957 CAGACGACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.26
18 10 0.32
19 13 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATATTTTTAAATTAAAT
Found at i:1027917 original size:10 final size:10
Alignment explanation
Indices: 1027904--1027941 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1027894 GAGAAGAGAG
*
1027904 AAGAAAACGA
1 AAGAAAATGA
1027914 AAGAAAATGA
1 AAGAAAATGA
*
1027924 AGGAAAATGA
1 AAGAAAATGA
1027934 AAGAAAAT
1 AAGAAAAT
1027942 TTTTTACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.68, C:0.03, G:0.21, T:0.08
Consensus pattern (10 bp):
AAGAAAATGA
Found at i:1028082 original size:6 final size:6
Alignment explanation
Indices: 1028071--1028098 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1028061 ATCAACCATG
1028071 CATTGC CATTGC CATTGC CATTGC CATT
1 CATTGC CATTGC CATTGC CATTGC CATT
1028099 TATTTCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.14, T:0.36
Consensus pattern (6 bp):
CATTGC
Found at i:1028341 original size:30 final size:31
Alignment explanation
Indices: 1028294--1028375 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
1028284 TATATCTTAT
* *
1028294 ATATATCATTTTG-TATTTAAATTTAATTTTA
1 ATAT-TCAATTTGATATTTAAATTTAACTTTA
* **
1028325 ATATTCAA-TTGATATTTAAGTTTCGCTTTA
1 ATATTCAATTTGATATTTAAATTTAACTTTA
*
1028355 ATATTCAATTTGATATCTAAA
1 ATATTCAATTTGATATTTAAA
1028376 CCAAATGGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 3 0.07
30 25 0.60
31 14 0.33
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.51
Consensus pattern (31 bp):
ATATTCAATTTGATATTTAAATTTAACTTTA
Found at i:1037897 original size:29 final size:30
Alignment explanation
Indices: 1037844--1037904 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
1037834 TGCAAGGCAA
*
1037844 AATTTCAAGATTCCGTTCCCTATTAAAAAC
1 AATTCCAAGATTCCGTTCCCTATTAAAAAC
* *
1037874 AATTCCAAGATTTC-TTTCCTATTAAAAAC
1 AATTCCAAGATTCCGTTCCCTATTAAAAAC
1037903 AA
1 AA
1037905 ATTTTTTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (30 bp):
AATTCCAAGATTCCGTTCCCTATTAAAAAC
Found at i:1040783 original size:30 final size:30
Alignment explanation
Indices: 1040744--1040807 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1040734 TGCAAGGAAA
*
1040744 AATTTCAAGAGTCCTTTCCCTATTAAAAAC
1 AATTCCAAGAGTCCTTTCCCTATTAAAAAC
* *
1040774 AATTCCAAGATTTCTTTCCCTATTAAAAAC
1 AATTCCAAGAGTCCTTTCCCTATTAAAAAC
1040804 AATT
1 AATT
1040808 TTTTGGGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.36
Consensus pattern (30 bp):
AATTCCAAGAGTCCTTTCCCTATTAAAAAC
Found at i:1053621 original size:39 final size:41
Alignment explanation
Indices: 1053520--1053703 Score: 197
Period size: 39 Copynumber: 4.6 Consensus size: 41
1053510 TTGAATGATG
* *
1053520 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
1053560 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
1053600 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* * *
1053639 TCCGGGTTAAGTCCCGAA-GCAATTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
1053678 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1053704 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
38 1 0.01
39 68 0.55
40 42 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:1053656 original size:79 final size:80
Alignment explanation
Indices: 1053520--1053703 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
1053510 TTGAATGATG
* *
1053520 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAA-GCAAT
1053584 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
1053599 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGCAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGCAA
*
1053661 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
1053678 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1053704 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 27 0.30
79 45 0.50
80 18 0.20
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGCAATT
GTGCGAGATACTATA
Found at i:1053726 original size:78 final size:77
Alignment explanation
Indices: 1053573--1053734 Score: 186
Period size: 78 Copynumber: 2.1 Consensus size: 77
1053563 GGACTAAGAT
* * **
1053573 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAA-GCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
1053638 ATCCGGGTTAAGTC
65 ATCCGGGTTAA-TC
* *
1053652 CCGAAGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CT
* *
1053715 ATATCC-GGTTAATT
63 AAATCCGGGTTAATC
1053729 CCGAAG
1 CCGAAG
1053735 GTACGTGATT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
77 9 0.12
78 33 0.46
79 30 0.42
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGAAGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
TCCGGGTTAATC
Done.